cookpa
commented
1 day ago First, perform tissue segmentation on the original space images to obtain the gray matter segmentation images. Then, use ANTs to register the images to standard space and transform the gray matter images to the standard space. Next, use the generated warp files to compute the Jacobian determinant, and multiply it with the standard-space gray matter images to obtain modulated gray matter in the standard space. Finally, conduct VBM analysis on these images.
This method is similar to SPM's VBM pipeline. Since ANTs generally provides better segmentation and registration results for animal data compared to SPM, I would like to ask the experts: is this pipeline feasible?
This sounds reasonable to me. SPM analyses usually build in spatial smoothing before analysis in the standard space. I am not sure exactly when in the pipeline they smooth the images, but it's hopefully documented in the code and / or papers.
Operating system and version
Ubuntu 20.04
CPU architecture
x86_64 (PC, Intel Mac, other Intel/AMD)
ANTs code version
ants-2.5.0
ANTs installation type
Downloaded Github release binaries
Summary of the problem
First, perform tissue segmentation on the original space images to obtain the gray matter segmentation images. Then, use ANTs to register the images to standard space and transform the gray matter images to the standard space. Next, use the generated warp files to compute the Jacobian determinant, and multiply it with the standard-space gray matter images to obtain modulated gray matter in the standard space. Finally, conduct VBM analysis on these images.
This method is similar to SPM's VBM pipeline. Since ANTs generally provides better segmentation and registration results for animal data compared to SPM, I would like to ask the experts: is this pipeline feasible?
Commands to reproduce the problem.
.
Output of the command with verbose output.
original space gm
standard space gm
modulated standard space gm
Data to reproduce the problem
.